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- EMDB-54214: Rab23 in complex with Fuzzy-Inturned -

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Basic information

Entry
Database: EMDB / ID: EMD-54214
TitleRab23 in complex with Fuzzy-Inturned
Map data
Sample
  • Complex: human Rab23 with GEF Fuzzy-Inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Protein inturned
    • Protein or peptide: Ras-related protein Rab-23
Keywordslongin domain / GEF / nucleotide exchange / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / craniofacial suture morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly ...negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / craniofacial suture morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly / ciliary transition zone / motile cilium assembly / embryonic skeletal system morphogenesis / negative regulation of cell division / positive regulation of cilium assembly / RAB geranylgeranylation / non-motile cilium assembly / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / GTP metabolic process / limb development / neural tube development / motile cilium / embryonic digit morphogenesis / hair follicle morphogenesis / smoothened signaling pathway / negative regulation of protein import into nucleus / roof of mouth development / autophagosome assembly / cilium assembly / regulation of ossification / hair follicle development / negative regulation of keratinocyte proliferation / cellular defense response / Hedgehog 'off' state / keratinocyte differentiation / vesicle-mediated transport / phagocytic vesicle / centriole / endomembrane system / phosphatidylinositol binding / autophagosome / negative regulation of cell migration / small monomeric GTPase / neural tube closure / intracellular protein transport / negative regulation of canonical Wnt signaling pathway / phagocytic vesicle membrane / cell junction / nervous system development / protein transport / cytoskeleton / endosome membrane / ciliary basal body / cilium / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / GTP binding / cell surface / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fuzzy protein / Protein inturned / Ras-related protein Rab-23 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain ...Fuzzy protein / Protein inturned / Ras-related protein Rab-23 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein fuzzy homolog / Ras-related protein Rab-23 / Protein inturned
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWilmes S / Schaefer J / Januliene D / Moeller A / Kuemmel D
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557-P10 Germany
German Research Foundation (DFG)SFB1557-P11 Germany
CitationJournal: To Be Published
Title: Mechanistic Adaptation of the Metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned
Authors: Wilmes S / Toenjes J / Drechsler M / Ruf A / Schaefer J / Luerick A / Januliene D / Apelt S / Di Iorio D / Wegner SV / Loose M / Moeller A / Paululat A / Kuemmel D
History
DepositionJun 30, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54214.png

Downloads & links

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Map

FileDownload / File: emd_54214.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0329
Minimum - Maximum-0.14107043 - 0.24603589
Average (Standard dev.)0.00019014096 (±0.0061901486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54214_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54214_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human Rab23 with GEF Fuzzy-Inturned

EntireName: human Rab23 with GEF Fuzzy-Inturned
Components
  • Complex: human Rab23 with GEF Fuzzy-Inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Protein inturned
    • Protein or peptide: Ras-related protein Rab-23

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Supramolecule #1: human Rab23 with GEF Fuzzy-Inturned

SupramoleculeName: human Rab23 with GEF Fuzzy-Inturned / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein fuzzy homolog

MacromoleculeName: Protein fuzzy homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.689883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS ...String:
VGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS GFAEAAGTTF VSLVVSGRVV AATEGWWRLG TPEAVLLPWL VGSLPPQTAR DYPVYLPHGS PTVPHRLLTL TL LPSLELC LLCGPSPPLS QLYPQLLERW WQPLLDPLRA CLPLGPRALP SGFPLHTDIL GLLLLHLELK RCLFTVEPLG DKE PSPEQR RRLLRNFYTL VTSTHFPPEP GPPEKTEDEV YQAQLPRACY LVLGTEEPGT GVRLVALQLG LRRLLLLLSP QSPT HGLRS LATHTLHALT PLL

UniProtKB: Protein fuzzy homolog

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Macromolecule #2: Protein inturned

MacromoleculeName: Protein inturned / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.526023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG VPRIPMASVA SCDSRPSSDE LPGDPSSQEE DEDYDFEDRV SDSGSYSSAS SDYDDLEPEW LDSVQKNGEL FYLELSEDE EESLLPETPT VNHVRFSENE IIIEDDYKER KKYEPKLKQF TKILRRKRLL PKRCNKKNSN DNGPVSILKH Q SNQKTGVI ...String:
MDYKDDDDKG VPRIPMASVA SCDSRPSSDE LPGDPSSQEE DEDYDFEDRV SDSGSYSSAS SDYDDLEPEW LDSVQKNGEL FYLELSEDE EESLLPETPT VNHVRFSENE IIIEDDYKER KKYEPKLKQF TKILRRKRLL PKRCNKKNSN DNGPVSILKH Q SNQKTGVI VQQRYKDVNV YVNPKKLTVI KAKEQLKLLE VLVGIIHQTK WSWRRTGKQG DGERLVVHGL LPGGSAMKSG QV LIGDVLV AVNDVDVTTE NIERVLSCIP GPMQVKLTFE NAYDVKRETS HPRQKKTQSN TSDLVKLLWG EEVEGIQQSG LNT PHIIMY LTLQLDSETS KEEQEILYHY PMSEASQKLK SVRGIFLTLC DMLENVTGTQ VTSSSLLLNG KQIHVAYWKE SDKL LLIGL PAEEVPLPRL RNMIENVIQT LKFMYGSLDS AFCQIENVPR LDHFFNLFFQ RALQPAKLHS SASPSAQQYD ASSAV LLDN LPGVRWLTLP LEIKMELDMA LSDLEAADFA ELSEDYYDMR RLYTILGSSL FYKGYLICSH LPKDDLIDIA VYCRHY CLL PLAAKQRIGQ LIIWREVFPQ HHLRPLADSS TEVFPEPEGR YFLLVVGLKH YMLCVLLEAG GCASKAIGSP GPDCVYV DQ VKTTLHQLDG VDSRIDERLA SSPVPCLSCA DWFLTGSREK TDSLTTSPIL SRLQGTSKVA TSPTCRRTLF GDYSLKTR K PSPSCSSGGS DNGCEGGEDD GFSPHTTPDA VRKQRESQGS DGLEESGTLL KVTKKKSTLP NPFHLGNLKK DLPEKELEI YNTVKLTSGP ENTLFHYVAL ETVQGIFITP TLEEVAQLSG SIHPQLIKNF HQCCLSIRAV FQQTLVEEKK KGLNSGDHSD SAKSVSSLN PVKEHGVLFE CSPGNWTDQK KAPPVMAYWV VGRLFLHPKP QELYVCFHDS VTEIAIEIAF KLFFGLTL

UniProtKB: Protein inturned

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Macromolecule #3: Ras-related protein Rab-23

MacromoleculeName: Ras-related protein Rab-23 / type: protein_or_peptide / ID: 3 / Details: N121I / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.492129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPLGSEFELL EEDMEVAIKM VVVGNGAVGK SSMIQRYCKG IFTKDYKKTI GVDFLERQIQ VNDEDVRLML WDTAGQEEFD AITKAYYRG AQACVLVFST TDRESFEAVS SWREKVVAEV GDIPTVLVQI KIDLLDDSCI KNEEAEALAK RLKLRFYRTS V KEDLNVNE ...String:
GPLGSEFELL EEDMEVAIKM VVVGNGAVGK SSMIQRYCKG IFTKDYKKTI GVDFLERQIQ VNDEDVRLML WDTAGQEEFD AITKAYYRG AQACVLVFST TDRESFEAVS SWREKVVAEV GDIPTVLVQI KIDLLDDSCI KNEEAEALAK RLKLRFYRTS V KEDLNVNE VFKYLAEKYL QKLKQQIAED PELTHSSSNK IGVFNTSGGS HSGQNSGTLN GGDVINLRPN KQRTKKNRNP FS SCSIP

UniProtKB: Ras-related protein Rab-23

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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